Package org.biojava.bio.seq

Interface StrandedFeature

All Superinterfaces:

Annotatable, Changeable, Feature, FeatureHolder

All Known Subinterfaces:

ComponentFeature, FramedFeature, HomologyFeature, RemoteFeature, RestrictionSite, RichFeature, SimilarityPairFeature

All Known Implementing Classes:

SimpleFramedFeature, SimpleHomologyFeature, SimpleRemoteFeature, SimpleRestrictionSite, SimpleRichFeature, SimpleSimilarityPairFeature, SimpleStrandedFeature

public interface StrandedFeature
extends Feature

Adds the concept of 'strand' to features.

Strandedness only applies to some types of sequence, such as DNA. Any implementation should blow chunks to avoid being added to a sequence for which strand is a foreign concept. Strand is intrinsicly part of all RichFeatures We strongly recommend using this interface.

Author:

Matthew Pocock

See Also:

RichFeature

Nested Class Summary

Nested Classes

Modifier and Type	Interface	Description
static class	StrandedFeature.Strand	Class to represent the 'strandedness' of a feature.
static class	StrandedFeature.Template	Template class for parameterizing the creation of a new StrandedFeature.

Nested classes/interfaces inherited from interface org.biojava.bio.Annotatable

Annotatable.AnnotationForwarder

Nested classes/interfaces inherited from interface org.biojava.bio.seq.Feature

Feature.ByLocationComparator

Nested classes/interfaces inherited from interface org.biojava.bio.seq.FeatureHolder

FeatureHolder.EmptyFeatureHolder

Field Summary

Fields

Modifier and Type	Field	Description
static StrandedFeature.Strand	NEGATIVE	Flag to indicate that a feature is on the negative strand.
static StrandedFeature.Strand	POSITIVE	Flag to indicate that a feature is on the positive strand.
static ChangeType	STRAND	The strand of this feature is being altered.
static StrandedFeature.Strand	UNKNOWN	Flag to indicate that a feature has an unknown strand.

Fields inherited from interface org.biojava.bio.Annotatable

ANNOTATION

Fields inherited from interface org.biojava.bio.seq.Feature

byLocationOrder, LOCATION, PROPERTY_DATA_KEY, SOURCE, SOURCETERM, TYPE, TYPETERM

Fields inherited from interface org.biojava.bio.seq.FeatureHolder

EMPTY_FEATURE_HOLDER, FEATURES, SCHEMA

Method Summary

Modifier and Type	Method	Description
StrandedFeature.Strand	getStrand()	Retrieve the strand that this feature lies upon.
SymbolList	getSymbols()	Return a list of symbols that are contained in this feature.
void	setStrand(StrandedFeature.Strand strand)	Set the strand that this feature lies upon.

Methods inherited from interface org.biojava.bio.Annotatable

getAnnotation

Methods inherited from interface org.biojava.utils.Changeable

addChangeListener, addChangeListener, isUnchanging, removeChangeListener, removeChangeListener

Methods inherited from interface org.biojava.bio.seq.Feature

features, getLocation, getParent, getSequence, getSource, getSourceTerm, getType, getTypeTerm, makeTemplate, setLocation, setSource, setSourceTerm, setType, setTypeTerm

Methods inherited from interface org.biojava.bio.seq.FeatureHolder

containsFeature, countFeatures, createFeature, filter, filter, getSchema, removeFeature

Field Detail

STRAND

static final ChangeType STRAND

The strand of this feature is being altered.

POSITIVE

static final StrandedFeature.Strand POSITIVE

Flag to indicate that a feature is on the positive strand.

NEGATIVE

static final StrandedFeature.Strand NEGATIVE

Flag to indicate that a feature is on the negative strand.

UNKNOWN

static final StrandedFeature.Strand UNKNOWN

Flag to indicate that a feature has an unknown strand.

Method Detail

getStrand

StrandedFeature.Strand getStrand()

Retrieve the strand that this feature lies upon.

This will be one of StrandedFeature.POSITIVE or NEGATIVE.

Returns:

one of the Strand constants

setStrand

void setStrand(StrandedFeature.Strand strand)
        throws ChangeVetoException

Set the strand that this feature lies upon.

This will be one of StrandedFeature.POSITIVE or NEGATIVE.

Parameters:

strand - a Strand.

Throws:

ChangeVetoException - if the strand may not be changed.

getSymbols

SymbolList getSymbols()

Return a list of symbols that are contained in this feature.

The symbols may not be contiguous in the original sequence, but they will be concatenated together in the resulting SymbolList.

The order of the Symbols within the resulting symbol list will be according to the concept of ordering within the location object.

If the feature is on the negative strand then the SymbolList will be reverse-complemented as appropriate.

Specified by:

getSymbols in interface Feature

Returns:

a SymbolList containing each symbol of the parent sequence contained within this feature in the order they appear in the parent